Note: xb12Ss with 35,000 miles. So original seals were well used.
Darin: Sorry to hear that. What you did matches my work. Yours actually looks a little cleaner.
I do not know what sensors are matched with ground A and which are ground B (see diagram I attached earlier). Or if ground A and B are connected. Perhaps your issue is with the "A" ground. But before hacking into the harness again, you can test. Before I hacked my harness, I stuck a very fine sewing needle into the terminal from the top side and made a temporary ground from the needle using alligator clips. I had to use wire cutters to get the right needle length (sticks out of terminal but is cleared by the seat). It was not 100% but the bike ran better - enough that I figured it was worth trying the extra ground. I put a drop of rubber cement on the hole when done.
In all of my research, i did learn two interesting things that might be affecting you:
1) The seals on the intake (throttle body) are known to fail and allow air to slip in. When my throttle body was pulled (replace the entire throttle body), the streaks on the head were visible where air was being sucked in. This would cause a lean condition. One of my hypothesis was that I had a vibration related air leak causing a lean condition and then the computer freaking out. Obviously, there was a ground issue but I cannot rule out the possibility that I also had an air seal issue.
2) Apparently, the coils can fail intermittently. You noted new plugs and injectors. Coil is easy to change and not terribly expensive.
Also:
3) TPS sensors can develop dead spots (all tps sensors, not just buell). In 24 years, I have replaced 3 TPS sensors on my firebird. A TPS in general should read 0.5 to 5 V from off to WOT. And it should be a linear with throttle. In the case of my Firebird, the sensors would fail in the just off idle range where you tend to have the throttle when cruising (i.e. largest percentage of time). Try measuring the output voltage and look for a dead spot. Go REALLY slowly and look for places where the output fluctuates faster than your hand.
I hope this helps...
Note: xb12Ss with 35,000 miles. So original seals were well used.